如何完成编码给定氨基酸序列的基因组的子串
肽编码问题包括寻找编码给定氨基酸序列的基因组的子串。
遗传密码描述了RNA 3聚体（密码子）翻译成20种不同氨基酸之一。 前三个圆圈从内向外移动，代表给定密码子的第一，第二和第三核苷酸。 第4，第5和第6个圆圈以三种方式定义翻译的氨基酸：氨基酸的全名，3个字母的缩写，以及单个字母的缩写。 64个总RNA密码子中的三个是终止密码子，其停止翻译并隐含地在氨基酸字母表中添加第21个终止符号。
问题在于拥有
输入：DNA字符串Text和氨基酸字符串Peptide。
和
输出：文本编码肽的所有子串（如果存在任何此类子串）。
Sample Input: ATGGCCATGGCCCCCAGAACTGAGATCAATAGTACCCGTATTAACGGGTGA MA Sample Output: ATGGCC GGCCAT ATGGCC 通过读取三元组获得结果， ATGGCC编码MA ， GGCCAT反向将CCGGTA反向写入，所以它实际上是ATGGCC （CCGGTA.reverse）
遗传密码的补充是CG，GC，TA和AT
所以为了解决这个问题，我首先使用已定义的数组
using System; using System.Collections.Generic; using System.Text; using System.Text.RegularExpressions; using System.Linq; using System.IO; using System.Collections; class Program { private static string[] CODONS = { "TTT", "TTC", "TTA", "TTG", "TCT", "TCC", "TCA", "TCG", "TAT", "TAC", "TGT", "TGC", "TGG", "CTT", "CTC", "CTA", "CTG", "CCT", "CCC", "CCA", "CCG", "CAT", "CAC", "CAA", "CAG", "CGT", "CGC", "CGA", "CGG", "ATT", "ATC", "ATA", "ATG", "ACT", "ACC", "ACA", "ACG", "AAT", "AAC", "AAA", "AAG", "AGT", "AGC", "AGA", "AGG", "GTT", "GTC", "GTA", "GTG", "GCT", "GCC", "GCA", "GCG", "GAT", "GAC", "GAA", "GAG", "GGT", "GGC", "GGA", "GGG", }; private static string[] AMINOS_PER_CODON = { "F", "F", "L", "L", "S", "S", "S", "S", "Y", "Y", "C", "C", "W", "L", "L", "L", "L", "P", "P", "P", "P", "H", "H", "Q", "Q", "R", "R", "R", "R", "I", "I", "I", "M", "T", "T", "T", "T", "N", "N", "K", "K", "S", "S", "R", "R", "V", "V", "V", "V", "A", "A", "A", "A", "D", "D", "E", "E", "G", "G", "G", "G", }; private static string[] AMINO_ABBREVIATIONS = { "F", "L", "I", "M", "V", "S", "P", "T", "A", "Y", "H", "Q", "N", "K", "D", "E", "C", "W", "R", "G" }; private static string[] FULL_NAMES = { "phenylalanine", "leucine", "isoleucine", "methionine", "valine", "serine", "proline", "threonine", "alanine", "tyrosine", "histidine", "glutamine", "asparagine", "lysine", "aspartic acid", "glutamic acid", "cysteine", "tryptophan", "arginine", "glycine" }; static void Main() { //then input is DNA string dna = ""; //The given peptide string givenPeptide = "KEVFEPHYY"; char[] givenPeptideArray = givenPeptide.ToCharArray() ; string codon=""; string auxCodon=""; string convertedCodon = ""; string clean = ""; int pivot = 0; int foundFlag = 0; string cleanReverse = ""; int foundFlagReverse = 0; string convertedCodonReverse = ""; //so the idea I was working was to loop dna string until getting to 3*givenPeptide.Length //because dna is red 3 by 3... //then get givenPeptide.Length and compare each char of given peptide with encoded //letter of scanned triplet //so for example first givenpeptide is 'M' so I would search for 'ATG' //then, if found increment a counter and then search for next 'GCC' etc... //however When testing with longer string I do not get complete result //I have for (int pos = 0; pos < dna.Length - (3*givenPeptide.Length) ; pos++) { pivot = pos; for (int codonPos = 0; codonPos < givenPeptide.Length; codonPos++) { codon = dna.Substring(pivot, 3); auxCodon = givenPeptideArray[codonPos].ToString(); convertedCodon = codonToAminoAcid(codon); convertedCodonReverse = codonToAminoAcid(DNAComplement(codon)); if (auxCodon.Equals(convertedCodon) ) { foundFlag++; clean += codon; } else { foundFlag = 0; clean = ""; } if (foundFlag == givenPeptide.Length) { Console.WriteLine(clean); foundFlag = 0; clean = ""; } //reverse if (auxCodon.Equals(convertedCodonReverse)) { foundFlagReverse++; cleanReverse += codon; } else { foundFlagReverse = 0; cleanReverse = ""; } if (foundFlagReverse == givenPeptide.Length) { Console.WriteLine(cleanReverse); foundFlagReverse = 0; cleanReverse = ""; } pivot+=3; } } }//end main public static string DNAComplement(string dna) { char[] array = dna.ToCharArray(); for (int i = 0; i < array.Length; i++) { char let = array[i]; if (let == 'A') array[i] = 'T'; else if (let == 'T') array[i] = 'A'; else if (let == 'C') array[i] = 'G'; else if (let == 'G') array[i] = 'C'; } Array.Reverse(array); return new string(array); } public static string codonToAminoAcid(String codon) { for (int k = 0; k < CODONS.Length ; k++) { if (CODONS[k].Equals (codon)) { return AMINOS_PER_CODON[k]; } } // never reach here with valid codon return "X"; } }//end class
我应该得到
AAGGAAGTATTTGAGCCTCATTATTAC AAAGAGGTGTTTGAACCTCATTACTAT AAGGAGGTATTTGAACCCCACTATTAC AAAGAAGTTTTCGAACCACATTATTAC AAGGAAGTGTTTGAACCTCACTATTAT AAAGAAGTTTTCGAGCCGCACTACTAC AAGGAAGTATTCGAACCACATTACTAT ATAATAATGCGGCTCGAATACTTCCTT GTAGTAATGGGGCTCGAAAACCTCCTT GTAGTAATGAGGTTCAAAAACCTCCTT GTAGTAATGGGGTTCGAAGACTTCCTT ATAATAGTGAGGCTCAAAAACTTCCTT ATAGTAATGGGGTTCGAAGACTTCCTT GTAGTAGTGCGGCTCAAAAACTTCCTT ATAGTAATGAGGTTCGAAAACCTCTTT ATAATAATGTGGCTCGAACACTTCTTT GTAGTAATGGGGCTCAAACACCTCTTT ATAGTAGTGAGGTTCGAAGACTTCCTT GTAATAGTGCGGTTCAAAAACTTCCTT ATAGTAGTGTGGTTCAAATACCTCCTT
但是我只得到：
AAGGAAGTATTTGAGCCTCATTATTAC AAAGAGGTGTTTGAACCTCATTACTAT AAGGAAGTGTTTGAACCTCACTATTAT AAAGAAGTTTTCGAGCCGCACTACTAC AAGGAGGTATTTGAACCCCACTATTAC AAAGAAGTTTTCGAACCACATTATTAC
我正在考虑问题，似乎问题是我每次都没有循环所有字符串…
看起来问题是双重的。 你的外部for循环不够远，无法捕获dna字符串的末尾。 其次，似乎逆转单个密码子不起作用，并且在获得补码之前必须取整个（givenPeptideLength * 3）字符串。 以下更改会输出您在示例中输入的字符串，因此我希望它能够满足您的需求。 它的优点还在于更加简洁。
using System; using System.Collections.Generic; using System.Text; using System.Text.RegularExpressions; using System.Linq; using System.IO; using System.Collections; namespace DNA { class Program { private static string[] CODONS = { "TTT", "TTC", "TTA", "TTG", "TCT", "TCC", "TCA", "TCG", "TAT", "TAC", "TGT", "TGC", "TGG", "CTT", "CTC", "CTA", "CTG", "CCT", "CCC", "CCA", "CCG", "CAT", "CAC", "CAA", "CAG", "CGT", "CGC", "CGA", "CGG", "ATT", "ATC", "ATA", "ATG", "ACT", "ACC", "ACA", "ACG", "AAT", "AAC", "AAA", "AAG", "AGT", "AGC", "AGA", "AGG", "GTT", "GTC", "GTA", "GTG", "GCT", "GCC", "GCA", "GCG", "GAT", "GAC", "GAA", "GAG", "GGT", "GGC", "GGA", "GGG", }; private static string[] AMINOS_PER_CODON = { "F", "F", "L", "L", "S", "S", "S", "S", "Y", "Y", "C", "C", "W", "L", "L", "L", "L", "P", "P", "P", "P", "H", "H", "Q", "Q", "R", "R", "R", "R", "I", "I", "I", "M", "T", "T", "T", "T", "N", "N", "K", "K", "S", "S", "R", "R", "V", "V", "V", "V", "A", "A", "A", "A", "D", "D", "E", "E", "G", "G", "G", "G", }; private static string[] AMINO_ABBREVIATIONS = { "F", "L", "I", "M", "V", "S", "P", "T", "A", "Y", "H", "Q", "N", "K", "D", "E", "C", "W", "R", "G" }; private static string[] FULL_NAMES = { "phenylalanine", "leucine", "isoleucine", "methionine", "valine", "serine", "proline", "threonine", "alanine", "tyrosine", "histidine", "glutamine", "asparagine", "lysine", "aspartic acid", "glutamic acid", "cysteine", "tryptophan", "arginine", "glycine" }; public static string DNAComplement(string dna) { char[] array = dna.ToCharArray(); for (int i = 0; i < array.Length; i++) { char let = array[i]; if (let == 'A') array[i] = 'T'; else if (let == 'T') array[i] = 'A'; else if (let == 'C') array[i] = 'G'; else if (let == 'G') array[i] = 'C'; } Array.Reverse(array); return new string(array); } public static string StringToAminoAcid(String input) { string result = ""; for (int i = 0; i < input.Length; i += 3) { result += codonToAminoAcid(input.Substring(i, 3)); } return result; } public static string codonToAminoAcid(String codon) { for (int k = 0; k < CODONS.Length; k++) { if (CODONS[k].Equals(codon)) { return AMINOS_PER_CODON[k]; } } // never reach here with valid codon return "X"; } static void Main() { //then input is DNA string dna = ""; //The given peptide string givenPeptide = "KEVFEPHYY"; int resultCount = 0; int candidateLength = givenPeptide.Length * 3; string forward = ""; string backward = ""; for (int pos = 0; pos < dna.Length - candidateLength + 1; pos++) // Added the "+ 1" { forward = dna.Substring(pos, candidateLength); backward = DNAComplement(forward); // Unremark to get a glimpse into what is happening... //Console.WriteLine("pos: {0}, forward: {1}, backward: {2}, forwardTranslation: {3}, backwardTranslation: {4}", // pos, forward, backward, StringToAminoAcid(forward), StringToAminoAcid(backward)); if ( (StringToAminoAcid(forward) == givenPeptide) || (StringToAminoAcid(backward) == givenPeptide) ) { resultCount++; Console.WriteLine(String.Format("Result {0,3} at position {1,6}... {2}", resultCount, pos, forward)); } } Console.WriteLine("Done"); Console.ReadLine(); }//end main }//end class }